Heng Li
|
50775362bb
|
r980: support auNGA
|
2020-04-10 21:36:59 -04:00 |
|
Heng Li
|
0a5e386359
|
r979: fixed asmgene wrong report. Resolves #581.
|
2020-04-06 19:57:15 -04:00 |
|
Heng Li
|
e2451e497a
|
r975: asmstat without CIGAR/NM
|
2020-03-22 19:16:43 -04:00 |
|
Heng Li
|
58c2251b18
|
compatibility with GenBank GTP (resolves $422)
|
2019-06-11 09:16:03 -04:00 |
|
Heng Li
|
7bc87b4175
|
Release minimap2-2.17 (r941)
|
2019-05-04 23:49:17 -04:00 |
|
Heng Li
|
f64e426a5a
|
r933: resume versioning
|
2019-04-28 17:05:37 -04:00 |
|
Heng Li
|
cdc730d573
|
gff2bed to output junction BED
|
2019-04-28 16:47:12 -04:00 |
|
Heng Li
|
6b391e3373
|
Release minimap2-2.16 (r922)
|
2019-02-28 15:49:24 -05:00 |
|
Heng Li
|
55e39c2d30
|
r921: output unmapped reads in full PAF
|
2019-02-27 15:03:19 -05:00 |
|
Heng Li
|
19208fb06b
|
r916: support long cs in sam-to-paf conversion
|
2019-02-17 09:35:23 -05:00 |
|
Heng Li
|
30abcf3cf9
|
r907: copy tag "cs" in sam2paf
Resolves #310
|
2019-01-13 17:52:31 -05:00 |
|
Heng Li
|
c404f49569
|
Release minimap2-2.15 (r905)
|
2019-01-10 12:34:45 -05:00 |
|
Heng Li
|
5b2fdfff9c
|
r895: option in asmgene to count autosomal only
|
2018-12-14 10:36:47 -05:00 |
|
Heng Li
|
eef1cee9b7
|
r893: added paftools.js vcfpair
|
2018-12-01 18:53:03 -05:00 |
|
Heng Li
|
62bbadf668
|
r887: fixed a bug in asmgene
|
2018-11-11 21:35:19 -05:00 |
|
Heng Li
|
cdaf46665a
|
r885: compute dup with asmstat
|
2018-11-07 00:26:05 -05:00 |
|
Heng Li
|
59f23f7579
|
Release minimap2-2.14 (r883)
|
2018-11-06 00:03:16 -05:00 |
|
Heng Li
|
09e089c3dc
|
r872: choose the longest isoform
|
2018-11-04 23:48:50 -05:00 |
|
Heng Li
|
e46cbb7d84
|
r871: print erroneous genes
|
2018-11-04 20:37:06 -05:00 |
|
Heng Li
|
57ec73ec6c
|
r870: separate <50% and <10%
|
2018-11-04 19:31:25 -05:00 |
|
Heng Li
|
9e27575387
|
r869: classify incomplete genes
|
2018-11-04 19:21:55 -05:00 |
|
Heng Li
|
b4ad8d8bf0
|
added asmgene
improvements coming; not made public yet
|
2018-11-04 17:24:05 -05:00 |
|
Heng Li
|
e315b9fada
|
hidden options to control bp calculation
|
2018-11-04 16:36:04 -05:00 |
|
Heng Li
|
5d5d392c02
|
Release minimap2-2.13 (r850)
|
2018-10-11 13:18:31 -04:00 |
Torsten Seemann
|
34be359e25
|
Add -s sample option for VCF output
|
2018-09-19 18:24:47 -04:00 |
|
Heng Li
|
5cfa621b2d
|
use unmapped records
|
2018-07-07 12:49:15 -05:00 |
|
Heng Li
|
bcf92b3c46
|
compute query coverage
|
2018-07-06 21:52:01 -05:00 |
|
Heng Li
|
097378ab90
|
reworked break point counting
|
2018-07-06 09:46:26 -04:00 |
|
Heng Li
|
10bbbe28c5
|
added asmstat
|
2018-07-05 13:22:32 -04:00 |
|
Heng Li
|
50dae10421
|
paftools call to show statistics on longer indels
|
2018-07-03 14:28:09 -04:00 |
|
Heng Li
|
39f836eac8
|
r767: don't crash when there is no "cg" (#153)
|
2018-04-24 12:32:37 -04:00 |
apregier
|
2e2e69107c
|
Small bugfix for paftools.js
The bug resulted in the wrong coverage being printed in some cases.
|
2018-04-04 16:29:54 -04:00 |
|
Heng Li
|
0bf97a367b
|
r755: junceval to only evaluate chromosomes
|
2018-03-24 23:10:06 -04:00 |
|
Heng Li
|
1c504d72e4
|
r754: option to only change name
|
2018-03-23 12:27:11 -04:00 |
|
Heng Li
|
242ff4e91d
|
r745: junceval - recognize "-" as file name
|
2018-03-15 12:51:46 -04:00 |
|
Heng Li
|
77ebd479f4
|
r743: added VCF output to "call"
|
2018-03-12 21:51:31 -04:00 |
|
Heng Li
|
ccaf12e1a2
|
r734: removed debugging print in call()
|
2018-03-09 23:46:21 -05:00 |
|
Heng Li
|
70428ca3a8
|
speedup tag parsing for sam2paf
|
2018-03-02 10:17:55 -05:00 |
|
Heng Li
|
9aea79d621
|
faster tag parsing
|
2018-03-02 10:09:14 -05:00 |
|
Heng Li
|
1770988627
|
make calling work with sam2paf output
|
2018-03-02 10:03:06 -05:00 |
|
Heng Li
|
2bfdad34bb
|
minor cleanup to last commit
|
2018-03-02 01:07:37 -05:00 |
|
Heng Li
|
953766cedd
|
generate cs; not carefully tested
|
2018-03-02 00:14:55 -05:00 |
|
Heng Li
|
dc61301d9f
|
sam2paf cleanup
|
2018-03-01 21:58:12 -05:00 |
|
Heng Li
|
e1f18690f6
|
paftools-r713: fixed bug for cov1 regions
|
2018-02-16 12:20:46 -05:00 |
|
Heng Li
|
3b17d62ccd
|
minor doc improvements
|
2018-02-12 22:27:02 -05:00 |
|
Heng Li
|
874b8c4795
|
rework misc/README; progressing but unfinished
|
2018-02-12 22:06:05 -05:00 |
|
Heng Li
|
f66de7df59
|
updated paftools revision number to r702
|
2018-02-12 11:39:04 -05:00 |
|
Heng Li
|
fbbd4e0968
|
changed output messages for clarity
|
2018-02-12 11:32:32 -05:00 |
|
Heng Li
|
8c89ba005e
|
merged cnt-feat into paftools
|
2018-02-12 11:29:42 -05:00 |
|
Heng Li
|
50775a1e6f
|
added liftOver
tested on a few toy examples
|
2018-02-12 11:12:23 -05:00 |
|
Heng Li
|
87cf650168
|
r697: fixed wrong #mapped reads in junceval
|
2018-02-09 18:45:57 -05:00 |
|
Heng Li
|
42dab6319b
|
don't call SNPs involving 'n'
|
2018-02-09 13:27:17 -05:00 |
|
Heng Li
|
8428809369
|
convert MUMmer's delta to PAF
|
2018-02-09 12:14:28 -05:00 |
|
Heng Li
|
642af5591e
|
merged intron-eval into paftools
|
2018-02-09 11:07:14 -05:00 |
|
Heng Li
|
2025a6279a
|
merged gff2bed and mapstat to paftools
|
2018-02-09 10:47:12 -05:00 |
|
Heng Li
|
3465b04724
|
merged a few converters to paftools
|
2018-02-09 10:23:30 -05:00 |
|
Heng Li
|
66c5e71fa8
|
merging scripts into one long script
|
2018-02-09 10:00:35 -05:00 |
|
Heng Li
|
dbf284b2d9
|
r684: separate end score from min_chain_score
|
2018-02-05 11:40:38 -05:00 |
|
Heng Li
|
3df5015668
|
General doc improvements
|
2018-02-02 21:45:46 -05:00 |
|
Heng Li
|
756379bf83
|
Documented paf2diff.js (more to come later)
|
2018-02-02 14:43:58 -05:00 |
|
Heng Li
|
41fd8a966a
|
Documented ov-eval.js
|
2018-02-02 14:18:18 -05:00 |
|
Heng Li
|
86e4933b1a
|
Added TOC
|
2018-02-02 14:12:30 -05:00 |
|
Heng Li
|
a633a744b6
|
more doc in misc
|
2018-02-02 14:07:17 -05:00 |
|
Heng Li
|
ddc31f57ba
|
Documented some k8 scripts; more coming
|
2018-02-02 13:57:08 -05:00 |
|
Heng Li
|
ad18fa490d
|
fixed typos
|
2018-01-30 10:11:50 -05:00 |
|
Heng Li
|
1842d7f5b5
|
allow to exclude regions
|
2018-01-07 22:35:56 -05:00 |
|
Heng Li
|
248b43cc47
|
work with targets in BED12
|
2018-01-07 19:39:25 -05:00 |
|
Heng Li
|
bf72969ab1
|
added a bed counter
I know there are tools for this purpose, but they don't quite meet my exact
need.
|
2018-01-07 15:19:18 -05:00 |
|
Heng Li
|
7b5a601d48
|
support paired-end reads
this gives unnecessary warnings, which will be fixed later.
|
2018-01-07 13:53:26 -05:00 |
|
Heng Li
|
e9607fcd9b
|
allow to convert read names
ONT read names are just too long and too hard to compress
|
2018-01-05 22:05:15 -05:00 |
|
Heng Li
|
a465a920ec
|
bug in block starts; added color and short-name
|
2018-01-05 21:45:56 -05:00 |
|
Heng Li
|
b20839be77
|
more robust ID conversion
|
2018-01-05 17:55:24 -05:00 |
|
Heng Li
|
209beb9955
|
convert EnsEMBL to UCSC name (optional)
|
2018-01-05 17:41:18 -05:00 |
|
Heng Li
|
cfe87f50c1
|
convert GTF/GFF3 to BED12
|
2018-01-05 17:10:43 -05:00 |
|
Heng Li
|
3a375d3436
|
renamed paf2ovlp to ov-eval
|
2017-12-24 18:04:00 -05:00 |
|
Heng Li
|
626f10e0d0
|
evaluate sensitivity in the same script
|
2017-12-24 17:55:42 -05:00 |
|
Heng Li
|
b997578078
|
find reads overlaps based on reference alignment
|
2017-12-24 17:20:27 -05:00 |
|
Heng Li
|
76206f574f
|
support both SAM and PAF as input
|
2017-12-02 21:57:19 -05:00 |
|
Heng Li
|
e575f884e1
|
convert spliced PAF to BED
|
2017-12-02 21:23:41 -05:00 |
|
Heng Li
|
cbdb6c069f
|
when there are incorrect anno, warn but not abort
|
2017-11-24 12:48:49 -05:00 |
|
Heng Li
|
39a9666246
|
convert PAF to LAST's cigar output
also added the support of BLAST-like output for "--cs=short".
|
2017-11-18 20:30:44 -05:00 |
|
Heng Li
|
662d05dc02
|
fixed incorrect var coordinate
|
2017-11-12 20:25:33 -05:00 |
|
Heng Li
|
379457c18b
|
use mapq threshold
|
2017-11-12 19:01:34 -05:00 |
|
Heng Li
|
03169d590b
|
print cov-1 regions (not BED output any more)
|
2017-11-12 18:45:49 -05:00 |
|
Heng Li
|
8c8d446820
|
find regions covered by one contig
|
2017-11-12 18:41:01 -05:00 |
|
Heng Li
|
0ddb064f17
|
dnadiff-like script; improvement coming
|
2017-11-12 15:07:29 -05:00 |
|
Heng Li
|
a13691d00d
|
eval script works with /[12] in SAM
|
2017-09-27 23:33:59 -04:00 |
|
Heng Li
|
92ec8bd859
|
added the /1 or /2 suffix
|
2017-09-26 12:04:35 -04:00 |
|
Heng Li
|
6a82a21dee
|
r361: improved mapq for short reads
|
2017-09-13 15:32:39 -04:00 |
|
Heng Li
|
240f6caaff
|
backup manuscript
|
2017-08-24 22:05:14 +08:00 |
|
Heng Li
|
ce859dbe1c
|
evaluate introns
this simplies the metrics
|
2017-08-20 21:54:59 +08:00 |
|
Heng Li
|
a4c41f64a5
|
the final version
to be replaced by intron-eval
|
2017-08-20 21:54:35 +08:00 |
|
Heng Li
|
5ed2faf270
|
minor tuning to the matching rules
|
2017-08-19 16:21:49 +08:00 |
|
Heng Li
|
2d11aaa830
|
option to print all exons for debugging
|
2017-08-12 10:04:16 -04:00 |
|
Heng Li
|
30b8cb4672
|
option to print correct exons
|
2017-08-11 17:50:21 -04:00 |
|
Heng Li
|
0c1760bc86
|
bugfix; print errors; better rules
|
2017-08-11 16:28:52 -04:00 |
|
Heng Li
|
a99358bc3d
|
r282: reduced intron cost; added eval script
|
2017-08-11 00:06:01 -04:00 |
|
Heng Li
|
5b10667967
|
sim-eval.js to support mason2 read names and SAM
|
2017-08-07 13:28:33 -04:00 |
|
Heng Li
|
bd1541dce1
|
renamed simulation-related scripts
|
2017-08-07 13:26:25 -04:00 |
|
Heng Li
|
1597f2b030
|
convert mason2 SAM to fastq
|
2017-08-07 12:45:34 -04:00 |